A single object in Blender = multiple objects in Pepakura
Assuming that you are using .obj file exange format, Pepakura will import the object exported from Blender as a single object if in blender you join all the geometry in a single object.

Pepakura is an unfolding software. Starting from the given geometry,it caluculates the angles and suggest where to put seams, add labels... but all rely on the initial geometry. If you give it two disconnected pieces, even if they are "the same object" they will be considered disconnected, so their boundaries will obiuvsly be seams.





Notice in the images above how pepakura ignores the fact that the cubes are intersected and cosider them as two disjoined cubes (as they are also in Blender, evon though they are stored in the same object).

You should work on your geometry and make all the pieces that you want be connected a whole.

You can use:


Boolean operations
Bridge edge loops, or add faces manually or with F2 add-on if the borders are distant
Remove doubles, if border are almost in the same place
etc...